This study is aimed at assessing the Cone-beam computed tomographic (CBCT) characteristics of temporomandibular joints (TMJ) in degenerative temporomandibular joint disease (DJD) patients with chewing side preference (CSP). CBCT images of 98 patients with DJD (67 with CSP and 31 without CSP) and 22 asymptomatic participants without DJD were measured retrospectively to compare the osteoarthritic changes and the morphology of TMJ. Quantitative analysis of the TMJ radiographic images was performed to present a comparison between the three inter-group groups and between the two sides of the joints. The frequencies of the articular flattening and surface erosion occur more often in the preferred side joints of DJD patients with CSP than the contralateral side. In addition, the horizontal angle of condyle, the depth of glenoid fossa (DGF), and the inclination of articular eminence (IAE) were larger in DJD patients with CSP than that in asymptomatic participants (p<0.05). Also, the condylar anteroposterior dimension of preferred side joints was significantly less than that of non-preferred side (p=0.026), while the width of condyles (p=0.041) and IAE (p=0.045) was greater. DJD patients with CSP appear to have a higher prevalence of osteoarthritic changes, with the morphological changes such as flat condyle, deep glenoid fossa, and steep articular eminence, which might be considered the characteristic imaging features. This study found that CSP is a predisposing factor for the development of DJD, and attention should be paid to the existence of CSP in DJD patients during the clinical practice.